- [performance] Replace retrieval of all event documents with aggregations #226
- [enhancement] Use requirements.txt in Docker build #255
- [enhancement] Add helpful descriptions, tooltips etc #248
- [enhancement] Remove interaction limit input field #246
- [enhancement] Show actual number of table pages #243
- [enhancement] Add the publication date to the index #233
- [bug][enhancement] Update argument1 and argument2 index fields with FamPlex, HGNC and equal name aggregate IDs #222
- [enhancement] (re)add fields for ES aggregations to index #208
- [enhancement] Update to ElasticSearch 7.17.8. #197
- [enhancement] Integrate GO -> gene mapping #187
- [enhancement] Integrate HGNC -> gene ID mapping #186
- [bug] Fix download crash for fulltext-only data #253
- [bug] Make copy button for download link work on Windows #249
- [bug] Normalize interaction arguments in Excel sheet argument statistics #245
- [bug] Reset retrieval of unary events in new session #236
- [bug] Investigate AKT search behavior #227
- [bug] Update concept manager for gene ontology correction #225
- [bug] Fix download button on the new ResultDownload page #217
- [bug] Take care to avoid AGGREGATE_EQUAL_NAMES nodes when fetching geneInfo #194
- [closed] Integrate UniProt Accession or Mnemomic -> NCBI Gene ID mapping #120
- [closed] Integrate ID mapping #117
- [bug] Fix NPE when entering the page via FAQ or Help page #223
- [enhancement] Offer a page for delayed results download #213
- [enhancement] Add a service to delete temporary Excel download files after a given amount of time #212
- [bug] Fix download file issue "file not found" in production container #220
- [bug] Fix truncated download table due to event download restriction for charts #215
- [closed] Download functionality #32
- [enhancement] Add an input field to allow the user the specification of the number of interactions used for aggregations #207
- Version 0.11.2. Fixes #207,#208. by @khituras in #209
- Issue68atid fix by @SchSascha in #82
- Rather a formal pull request, just to keep the documentation style up and running by @SchSascha in #87
- Table Download now results in an xls file (realized with apache poi).… by @fmatthies in #90
- 0.2 sankey d3 by @khituras in #109
- 0.2 by @khituras in #110
- Tab sessions by @khituras in #137
- Result paging by @khituras in #142
- State of BioArxiv first version by @khituras in #148
- Add python to the docker image. Fixes #152. by @khituras in #153
- 0.9.0 beta by @khituras in #158
- Fix #200, the pure section heading search crash. by @khituras in #201
- Interactive help by @khituras in #206
- [performance] Add an index document field for aggregations #181
- [enhancement] Provide search examples #196
- [enhancement] Introduce separate waiting-for-data state for paged requests #193
- [enhancement] Load geneInfo in batch instead of one-by-one #192
- [enhancement] Add a mechanism for GePiFamplexIdAssigner to let GNP decide whether a gene should be mapped to Famplex/HGNC groups or not #191
- [enhancement] Switch FamPlex and HGNC IDs in the index from conceptIds to prefixed original IDs #190
- [enhancement] Extend preferredName normalization to punctuation and white spaces #188
- [enhancement] Add taxIds to index documents and filter on those #185
- [enhancement] Show message when concrete gene IDs and tax IDs are given with contradictions #184
- [enhancement] Make direct links possible #182
- [enhancement] Create index documents for unary events #180
- [enhancement] Filter out duplicates based on abbreviation introduction #179
- [enhancement] Integrate factuality (level of likelihood that an interaction actually takes place) #173
- [enhancement] Add hover effects and tooltips for sankey diagrams #172
- [enhancement] Add 6th Bootstrap grid tier #171
- [enhancement] Distribute widgets relative to breakpoints and available space #170
- [enhancement] Display messages in widges when there is no data #169
- [enhancement] Try to resolve genes by synonym if there is no match by preferredName/symbol #168
- [enhancement] Add bar plot widget #166
- [enhancement] Always show 'others' slice in pie charts when there are too many genes to show #165
- [enhancement] Make sankey diagrams so that their contents are not cropped #155
- [enhancement] Integrate Gene Name -> NCBI Gene ID mapping #118
- [bug] Deactivate B list file upload as long as A is empty #147
- [bug] Make the event type filter work for 'phosphorylation' #144
- [bug] Fix issue where b-list cannot be read from file repeatedly #134
- [evaluation] Add a UIMA BioNLP ST gene merger component #178
- [evaluation] Add code to evaluate BioSem given GNormPlus genes #177
- [evaluation] Add code to reproduce GNormPlus evalution results in the GePI paper #176
- [closed] Common partners Sankey: hide non-common edges #167
- [closed] Check if reflexive relations are returned #131
- [closed] Integrate Ensemble ID -> NCBI Gene ID mapping #119
- [closed] Remove the organism restriction of GeNo #112
- [closed] Make diagrams always use up the available space #101
- [bug] Fix null context with paragraph filter #164
- [enhancement] Add tabs to the pie charts widgets to switch between a- and b-counts #162
- [enhancement] Scroll to top upon search submission #161
- [enhancement] Implement AND/OR for sentence and paragraph filters #160
- [enhancement] Fix Pie Chart coloring #156
- [performance] Implement paged result retrieval for closed search #151
- [performance] Avoid complete result download after each search #150
- [enhancement] Avoid freezing on result download #157
- [enhancement] Re-enable the common partners Sankey #149
- [enhancement] Make the table Ajax-Enabled #143
- [enhancement] Implement paged result retrieval from ES #138
- [bug] Fix bug where events are duplicated #133
- [closed] Add highlighting to table #129
- [closed] Allow sentence and paragraph filters to contain compounds/phrases #125
- [closed] Add paragraph filter options to GepiInput #124
- [closed] Make paragraph text information available for all events #123
- [bug] Fix download table creation #152
This is the state of GePI right after the publication of the first bioRxiv version.
- [bug] references are missing (got deleted to aid sentence splitter) #92
- [bug] atid shown in results instead of gene symbol #68
- [bug] events.argumentsearch does not recognise atids. #60
- [bug] multiple line entries #15
- [closed] Add pipeline to create test data. #139
- [closed] Create specific argument1 and argument2 fields. #132
- [closed] Allow all events to be retrieved filtered on sentence/paragraph #126
- [closed] Update to Java 11 #121
- [closed] Erik Changelog 0.1.18-43 #99
- [closed] Erik Changelog 0.1.18-42 #98
- [closed] Erik Changelog 0.1.18-41 #96
- [closed] Integrate search for relation type #94
- [closed] General changelog #86
- [closed] Come up with a solution for the problem of gene db data export #83
- [closed] Bernd changelog 0.1.17-49 #80
- [closed] Sascha changelog 0.1.17-49 #78
- [closed] explicitely evaluate Sankey plot with common partners #77
- [closed] remove bar plot/widget #75
- [closed] extract neo4jDB concept project #73
- [closed] Add main event type to result table #71
- [closed] Add resource versioning #70
- [closed] Allow to download table also in format xls #64
- [closed] order of mentioned gene events #62
- [closed] clean up gepi neo4j build up scripts #57
- [closed] Download feature for table #54
- [closed] provide filter possibilities to narrow down search / for search exploration #49
- [closed] Provide article id in resulting table per sentence #41
- [closed] Search box entries A|B should automatically be extended to all homologous genes #39
- [closed] proper Inject usage for googleChartManager #38
- [closed] correct table resizing #31
- [closed] Input list recoverable from left side #30
- [closed] pie chart resizing #29
- [closed] Full index gepi available on coling servers #28
- [closed] complete medline & pmc index #27
- [closed] working demo on Sascha's laptop #26
- [closed] workable A - B Search #25
- [closed] input field - responsiveness #24
- [closed] bar diagram - numbers #23
- [closed] Table pager #22
- [closed] elasticsearch index: pmid/pmcid fields wrong? #21
- [closed] event class - atid order in meaningful order? #20
- [closed] Switch to an event-centric index structure #19
- [closed] Add index field for number of arguments #17
- [closed] es_query - no pmc hits #16
- [closed] atid's #14
- [closed] Result Portal #13
- [closed] PMC XMI Parsing issue: Maximum attribute size limit exceeded #11
- [closed] Problematic Medline Document: 23700993 #10
- [closed] Point to missing and useful documentation #8
- [closed] Build Gene Database #6
- [closed] jpp: jules-longdocument-skipper (jls) #5
- [closed] Who does what? #4
- [closed] Current status of modules relevant for GePi #3
- [closed] Write FieldsGenerator #2
- [closed] result pane small #1
- [enhancement] Support multiple sources for relations and genes #146
- [enhancement] Support event indexing for multiple IDs per gene #145
- [enhancement] Add a PieChart again #141
- [enhancement] Enable section heading filter #140
- [enhancement] Add filter terms to the Excel frontpage #135
- [urgent] Update data download to the format used in latest data deliveries #115